confab: confab.xml annotate

annotate confab.xml @ 20:df8c4f142ae3

ChemicalToolBoX update.

author	Bjoern Gruening <bjoern.gruening@gmail.com>
date	Tue, 23 Jul 2013 14:53:58 +0200
parents	a396884f933a
children	ff23947232d0

rev	line source
17 6eb2a0358b9c ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 4 diff changeset	1 <tool id="ctb_confab" name="Conformer calculation" version="0.1">
0 ea7816847e5e Uploaded bgruening parents: diff changeset	2 <description>for molecules (confab)</description>
4 6c8f72ee4a51 Uploaded bgruening parents: 2 diff changeset	3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile"></parallelism>
0 ea7816847e5e Uploaded bgruening parents: diff changeset	4 <requirements>
ea7816847e5e Uploaded bgruening parents: diff changeset	5 <requirement type="package" version="1.0.1">confab</requirement>
ea7816847e5e Uploaded bgruening parents: diff changeset	6 </requirements>
ea7816847e5e Uploaded bgruening parents: diff changeset	7 <command> confab
ea7816847e5e Uploaded bgruening parents: diff changeset	8 -i ${infile.ext}
ea7816847e5e Uploaded bgruening parents: diff changeset	9 -o sdf
ea7816847e5e Uploaded bgruening parents: diff changeset	10 -r $RMSD
ea7816847e5e Uploaded bgruening parents: diff changeset	11 -e $energy
ea7816847e5e Uploaded bgruening parents: diff changeset	12 -c $conformers
ea7816847e5e Uploaded bgruening parents: diff changeset	13 $first_conformer
ea7816847e5e Uploaded bgruening parents: diff changeset	14 $infile
ea7816847e5e Uploaded bgruening parents: diff changeset	15 $outfile 2>&1
ea7816847e5e Uploaded bgruening parents: diff changeset	16 </command>
ea7816847e5e Uploaded bgruening parents: diff changeset	17 <inputs>
17 6eb2a0358b9c ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 4 diff changeset	18 <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates" help="Dataset missing? See TIP below"/>
0 ea7816847e5e Uploaded bgruening parents: diff changeset	19 <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (in Angstrom)' />
ea7816847e5e Uploaded bgruening parents: diff changeset	20 <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' />
17 6eb2a0358b9c ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 4 diff changeset	21 <param name='conformers' type='integer' value='100' label='Max number of conformers to test' />
6eb2a0358b9c ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 4 diff changeset	22 <param name='first_conformer' type='boolean' truevalue='-a' falsevalue='' label='Include the input conformation as the first conformer' />
0 ea7816847e5e Uploaded bgruening parents: diff changeset	23 </inputs>
ea7816847e5e Uploaded bgruening parents: diff changeset	24 <outputs>
2 e7bb18ef7f54 Uploaded bgruening parents: 0 diff changeset	25 <data format="sdf" name="outfile" label="${tool.name} on ${on_string}"/>
0 ea7816847e5e Uploaded bgruening parents: diff changeset	26 </outputs>
ea7816847e5e Uploaded bgruening parents: diff changeset	27 <tests>
ea7816847e5e Uploaded bgruening parents: diff changeset	28 <test>
ea7816847e5e Uploaded bgruening parents: diff changeset	29 <param name="infile" value='CID_3033.sdf' ftype='sdf' />
ea7816847e5e Uploaded bgruening parents: diff changeset	30 <param name='RMSD' value='0.5' />
ea7816847e5e Uploaded bgruening parents: diff changeset	31 <param name='energy' value='50.0' />
ea7816847e5e Uploaded bgruening parents: diff changeset	32 <param name='conformers' value='100000' />
ea7816847e5e Uploaded bgruening parents: diff changeset	33 <param name='first_conformer' value='-a' />
ea7816847e5e Uploaded bgruening parents: diff changeset	34 <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' />
ea7816847e5e Uploaded bgruening parents: diff changeset	35 </test>
ea7816847e5e Uploaded bgruening parents: diff changeset	36 </tests>
ea7816847e5e Uploaded bgruening parents: diff changeset	37 <help>
ea7816847e5e Uploaded bgruening parents: diff changeset	38
18 a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	39 .. class:: infomark
0 ea7816847e5e Uploaded bgruening parents: diff changeset	40
18 a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	41 What this tool does
0 ea7816847e5e Uploaded bgruening parents: diff changeset	42
18 a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	43 Confab_ is a conformation generator. The algorithm starts with an input 3D structure which, after some initialisation steps, is used to generate multiple conformers which are filtered on-the-fly to identify diverse low energy conformers.
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	44
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	45 .. _Confab: https://code.google.com/p/confab/
0 ea7816847e5e Uploaded bgruening parents: diff changeset	46
ea7816847e5e Uploaded bgruening parents: diff changeset	47 -----
ea7816847e5e Uploaded bgruening parents: diff changeset	48
18 a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	49 .. class:: infomark
0 ea7816847e5e Uploaded bgruening parents: diff changeset	50
18 a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	51 Input
0 ea7816847e5e Uploaded bgruening parents: diff changeset	52
18 a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	53 * Example::
0 ea7816847e5e Uploaded bgruening parents: diff changeset	54
18 a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	55 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	56 21.2410 9.4460 64.5510 C 0 0 0 0 0 0 0 0 0 0 0 0
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	57 22.0000 8.1250 64.6300 C 0 0 0 0 0 0 0 0 0 0 0 0
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	58 21.7010 7.3010 65.5120 O 0 0 0 0 0 0 0 0 0 0 0 0
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	59 23.1180 7.8720 63.7340 C 0 0 0 0 0 0 0 0 0 0 0 0
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	60 23.4530 8.7270 62.7850 C 0 0 0 0 0 0 0 0 0 0 0 0
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	61 24.6970 8.4430 61.9510 C 0 0 0 0 0 0 0 0 0 0 0 0
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	62
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	63 .......
0 ea7816847e5e Uploaded bgruening parents: diff changeset	64
18 a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	65 1 2 1 0 0 0 0
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	66 1 11 1 0 0 0 0
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	67 2 3 1 0 0 0 0
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	68 3 4 2 0 0 0 0
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	69 3 5 1 0 0 0 0
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	70 5 6 2 0 0 0 0
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	71 6 7 1 0 0 0 0
0 ea7816847e5e Uploaded bgruening parents: diff changeset	72
18 a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	73 RMSD cutoff (in Angstrom) 0.5
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	74 Energy cutoff (in kcal/mol) 50.0
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	75 Max number of conformers to test 100000
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	76 Include the input conformation as the first conformer False
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	77
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	78 -----
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	79
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	80 .. class:: infomark
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	81
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	82 Output
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	83
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	84 * Example::
0 ea7816847e5e Uploaded bgruening parents: diff changeset	85
ea7816847e5e Uploaded bgruening parents: diff changeset	86 23 26 0 0 0 0 0 0 0 0999 V2000
ea7816847e5e Uploaded bgruening parents: diff changeset	87 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	88 21.2410 9.4460 64.5510 C 0 0 0 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	89 22.0000 8.1250 64.6300 C 0 0 0 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	90 21.7010 7.3010 65.5120 O 0 0 0 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	91 23.1180 7.8720 63.7340 C 0 0 0 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	92 23.4530 8.7270 62.7850 C 0 0 0 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	93 24.6970 8.4430 61.9510 C 0 0 0 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	94 24.4490 8.6370 60.4430 C 0 0 0 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	95 23.7890 9.9970 60.0980 C 0 0 2 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	96 22.4340 10.0950 60.8720 C 0 0 1 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	97 22.6140 10.0230 62.4340 C 0 0 1 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	98 21.6330 11.3540 60.4500 C 0 0 0 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	99 21.4320 11.4340 58.9110 C 0 0 0 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	100 22.7860 11.4040 58.1690 C 0 0 1 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	101 23.4830 10.0600 58.5980 C 0 0 1 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	102 24.6740 9.9180 57.6180 C 0 0 0 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	103 24.0720 10.4500 56.2670 C 0 0 0 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	104 22.7140 11.1490 56.6270 C 0 0 2 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	105 23.6590 12.6770 58.4540 C 0 0 0 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	106 23.4270 11.2460 63.0070 C 0 0 0 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	107 22.3750 12.3880 55.7810 C 0 0 0 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	108 23.2120 12.8760 55.0520 O 0 0 0 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	109 21.0090 12.9760 55.8570 C 0 0 0 0 0 0 0 0 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	110
ea7816847e5e Uploaded bgruening parents: diff changeset	111 ::
ea7816847e5e Uploaded bgruening parents: diff changeset	112
ea7816847e5e Uploaded bgruening parents: diff changeset	113 1 2 1 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	114 1 11 1 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	115 2 3 1 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	116 3 4 2 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	117 3 5 1 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	118 5 6 2 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	119 6 7 1 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	120 6 11 1 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	121 7 8 1 0 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	122 9 8 1 6 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	123 10 9 1 1 0 0 0
ea7816847e5e Uploaded bgruening parents: diff changeset	124
18 a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	125 -----
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	126
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	127 .. class:: infomark
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	128
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	129 Cite
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	130
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	131 Confab_
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	132
a396884f933a ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 17 diff changeset	133 .. _Confab: https://code.google.com/p/confab/
0 ea7816847e5e Uploaded bgruening parents: diff changeset	134
ea7816847e5e Uploaded bgruening parents: diff changeset	135
ea7816847e5e Uploaded bgruening parents: diff changeset	136 </help>
ea7816847e5e Uploaded bgruening parents: diff changeset	137
ea7816847e5e Uploaded bgruening parents: diff changeset	138 </tool>

Mercurial > repos > bgruening > confab

annotate confab.xml @ 20:df8c4f142ae3